[gmx-users] How VMD to display the velocity

[Höfling Martin]

Am 05.03.2009 um 07:44 schrieb Dechang Li:

Not sure about VMD, but you can write a short script for pymol in  
python:

1: reading velocities from gro
2: converting gro2pdb
3: read in pdb into pymol
4: create cgo object containing arrow (search in the list archives or  
on the wiki page of pymol)

Best
	Martin

Snippet for step 2 and 3:

def gro( fnm , name=None,state=1):
     '''
     Loads a gro gromacs File
     @param fnm: filename to load
     @param name: Name of object
     @param state: state to load to
     '''
     tmpfile=mktemp(".pdb")
     comd="editconf -f %s -o %s" % (fnm,tmpfile)
     if os.system(comd):
         print "Running command %s failed"%comd
         return False

     if name ==None:
         cmd.load(tmpfile, fnm[:-4] ,state=state)
     else:
         cmd.load(tmpfile,name,state=state)
     os.remove(tmpfile)
     return True


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